TOol for Motif TO Motif comparison (TOMTOM)

For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net.

If you use TOMTOM in your research, please cite the following paper:
Shobhit Gupta, JA Stamatoyannopolous, Timothy Bailey and William Stafford Noble, "Quantifying similarity between motifs", Genome Biology, 8(2):R24, 2007.

Query Motifs  |  Target Databases  |  Matches  |  Program information  |  Explanation

Query Motifs

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Name 

Preview 

Matches 

List 

1_e_k36me3_26_0.625
GGCGTGAGCC
0
2_e_k36me3_0_0.624
ACGCCTGTA
0
3_e_k36me3_55_0.615
CAGCTACTCA
0
4_e_k36me3_97_0.611
TCGCTTGAA
0
5_e_k36me3_11_0.611
CAGTGGCGCGAT
0
6_e_k36me3_5_0.608
CGTCTCTAC
0
7_e_k36me3_109_0.606
AAGTGCTGG
0
8_e_k36me3_13_0.605
AACCCCGTC
0
9_e_k36me3_125_0.604
GTCTCAAAAAA
0
10_e_k36me3_24_0.599
AGGAGTTCG
1 RPC155_01_M01798_T
11_e_k36me3_115_0.598
AGGTGATCC
0
12_e_k36me3_118_0.597
GGCAACATAG
0
13_e_k36me3_163_0.591
AGTACAGTG
0
14_e_k36me3_86_0.588
CACCGTGCC
0
15_e_k36me3_152_0.585
CAAGACCAG
0
16_e_k36me3_96_0.583
GATCGCACC
0
17_e_k36me3_141_0.580
AGAATCACT
0
18_e_k36me3_160_0.576
AAGCAATTC
0
19_e_k36me3_140_0.574
GAGCAAGAC
0
20_e_k36me3_225_0.570
CATACCTGGT
0
21_e_k36me3_169_0.568
ACCAACATG
0
22_e_k27ac_194_0.567
AAGGCAGGA
0
23_e_k36me3_150_0.567
CTCCTGGGC
0
24_e_k36me3_193_0.559
GGCCAGGCA
0
25_e_k36me3_187_0.559
AAGATCGTG
0
26_e_k9me3_166_0.448
GGGTGGGGAC
0
27_h_k9me3_22_0.448
TGGAAACGGG
3 DIS3_8_H,  MAGED4_4_H,  MYLK_6_H
28_e_k36me3_174_0.550
ACGTTGGCC
0
29_e_k4me3_202_0.549
ACTCGGAA
0
30_e_k36me3_172_0.548
CGTACGGC
0
31_h_k9me3_1_0.452
AATGCACACATC
0
32_h_k36me3_14_0.548
TTAAGTAGTACT
0
33_e_k9me3_42_0.454
GAGATGAACA
0
34_e_k36me3_233_0.544
CGTATCAGA
0
35_e_k36me3_136_0.543
CCGTGTTAG
0
36_e_k27ac_7_0.457
CTCTCTCTCA
0
37_e_k9me3_87_0.458
AAATATCTTC
0
38_e_k27me3_37_0.459
GAGCGCGCA
0
39_h_k4me1_18_0.540
TACTGCTGAC
0
40_e_k36me3_237_0.540
AGGTACATG
0
41_h_k27me3_11_0.461
TTCGCTCCGA
1 MED-1_POL013.1_J
42_e_k4me3_73_0.539
AAGATGGCG
1 REX1_03_M01744_T
43_h_k27ac_12_0.462
GGGAAGGAATTT
0
44_e_k36me3_216_0.537
CTGTCGCCA
0
45_e_k9me3_11_0.463
TGGCCGAAT
0
46_h_k9me3_16_0.464
GGGAACTCCCTG
2 NF-kappaB_MA0061.1_J,  NFKAPPAB_01_M00054_T
47_e_k4me3_56_0.465
GCGGGACCCG
0
48_e_k27me3_131_0.465
GCTCAGAGAG
0
49_h_k36me3_12_0.534
TCTTCAGAAG
0
50_e_k9me3_10_0.467
CCTATTCGG
1 BAT4_2_H
51_e_k4me3_308_0.533
TACGTAAA
0
52_h_k9me3_8_0.467
ATCTCACTCGGG
0
53_e_k36me3_205_0.530
ATCATCATCAG
0
54_h_k9me3_7_0.470
GACAGTGGGTGC
0
55_e_k9me3_142_0.470
CAGCTCCCAC
0
56_e_k9me3_112_0.472
CAAATGTCC
0
57_e_k36me3_220_0.528
AATCGTATC
0
58_e_k27me3_65_0.473
CCGCGGACA
2 NRSF_Q4_M01028_T,  PDR1_02_M01633_T
59_e_k27ac_405_0.473
GAACAATGG
7 SOX9_MA0077.1_J,  SOX9_B1_M00410_T,  ROX1_MA0371.1_J,  D_MA00445.1_J,  Sox30_primary_SCI09_U,  ROX1_Q6_M00728_T,  SOX4_01_M01308_T
60_e_k4me3_64_0.527
CGGCCGGCC
1 RDS1_MA0361.1_J
61_e_k4me3_309_0.526
AAATAACGT
0
62_h_k4me3_11_0.475
CACGCGAAAGGT
2 SWI4_01_M01609_T,  SWI4_MA0401.1_J
63_h_k4me3_5_0.523
TAAACGTT
0
64_e_k9me3_269_0.477
CAAACCATA
1 STUB1_11_H
65_e_k4me3_70_0.479
CGCGACGG
0
66_e_k27ac_480_0.479
AATAAACCT
0
67_e_k9me3_225_0.479
AGCCATGTGA
0
68_e_k27me3_277_0.479
TCCATTTTAC
0
69_h_k27ac_13_0.520
GTTAATCAGC
1 IVD_4_H
70_e_k9me3_95_0.481
GATAGAGCA
0
71_e_k27ac_467_0.482
CACAAGGAAA
0
72_e_k9me3_26_0.482
CACATCACAT
0
73_e_k4me3_274_0.516
GAGACGGTA
0
74_e_k27me3_309_0.485
CGTCTTTTC
0
75_e_k27ac_154_0.515
AGGCCTGACT
0
76_e_k27ac_470_0.514
CAGACTCTC
0
77_e_k9me3_84_0.487
AGGCCTCAA
0
78_e_k4me1_503_0.508
CATTTGGCA
0
79_h_k9me3_4_0.493
GGTACCGGGTTC
0
80_e_k4me1_254_0.507
CAGAGCATC
0

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiCmbned3.meme 2921 23

Matches to Query: 1_e_k36me3_26_0.625

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Matches to Query: 2_e_k36me3_0_0.624

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Matches to Query: 3_e_k36me3_55_0.615

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Matches to Query: 4_e_k36me3_97_0.611

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Matches to Query: 5_e_k36me3_11_0.611

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Matches to Query: 6_e_k36me3_5_0.608

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Matches to Query: 7_e_k36me3_109_0.606

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Matches to Query: 8_e_k36me3_13_0.605

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Matches to Query: 9_e_k36me3_125_0.604

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Matches to Query: 10_e_k36me3_24_0.599

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Summary 

Alignment 

Name RPC155_01_M01798_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.3742e-05
E-value 0.0401403
q-value 0.0802807
Overlap 9
Offset 2
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 11_e_k36me3_115_0.598

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Matches to Query: 12_e_k36me3_118_0.597

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Matches to Query: 13_e_k36me3_163_0.591

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Matches to Query: 14_e_k36me3_86_0.588

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Matches to Query: 15_e_k36me3_152_0.585

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Matches to Query: 16_e_k36me3_96_0.583

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Matches to Query: 17_e_k36me3_141_0.580

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Matches to Query: 18_e_k36me3_160_0.576

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Matches to Query: 19_e_k36me3_140_0.574

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Matches to Query: 20_e_k36me3_225_0.570

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Matches to Query: 21_e_k36me3_169_0.568

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Matches to Query: 22_e_k27ac_194_0.567

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Matches to Query: 23_e_k36me3_150_0.567

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Matches to Query: 24_e_k36me3_193_0.559

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Matches to Query: 25_e_k36me3_187_0.559

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Matches to Query: 26_e_k9me3_166_0.448

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Matches to Query: 27_h_k9me3_22_0.448

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Summary 

Alignment 

Name DIS3_8_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.72129e-06
E-value 0.0079489
q-value 0.015778
Overlap 7
Offset -1
Orientation Normal
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Summary 

Alignment 

Name MAGED4_4_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.34621e-05
E-value 0.0393229
q-value 0.0251818
Overlap 6
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MYLK_6_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.34621e-05
E-value 0.0393229
q-value 0.0251818
Overlap 6
Offset 0
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 28_e_k36me3_174_0.550

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Matches to Query: 29_e_k4me3_202_0.549

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Matches to Query: 30_e_k36me3_172_0.548

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Matches to Query: 31_h_k9me3_1_0.452

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Matches to Query: 32_h_k36me3_14_0.548

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Matches to Query: 33_e_k9me3_42_0.454

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Matches to Query: 34_e_k36me3_233_0.544

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Matches to Query: 35_e_k36me3_136_0.543

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Matches to Query: 36_e_k27ac_7_0.457

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Matches to Query: 37_e_k9me3_87_0.458

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Matches to Query: 38_e_k27me3_37_0.459

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Matches to Query: 39_h_k4me1_18_0.540

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Matches to Query: 40_e_k36me3_237_0.540

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Matches to Query: 41_h_k27me3_11_0.461

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Summary 

Alignment 

Name MED-1_POL013.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.74179e-06
E-value 0.0138508
q-value 0.0277015
Overlap 6
Offset -3
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 42_e_k4me3_73_0.539

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Summary 

Alignment 

Name REX1_03_M01744_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.0053e-05
E-value 0.0293648
q-value 0.0587295
Overlap 9
Offset 0
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 43_h_k27ac_12_0.462

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Matches to Query: 44_e_k36me3_216_0.537

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Matches to Query: 45_e_k9me3_11_0.463

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Matches to Query: 46_h_k9me3_16_0.464

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Summary 

Alignment 

Name NF-kappaB_MA0061.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.49702e-05
E-value 0.0437278
q-value 0.0418022
Overlap 10
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name NFKAPPAB_01_M00054_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.49702e-05
E-value 0.0437278
q-value 0.0418022
Overlap 10
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 47_e_k4me3_56_0.465

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Matches to Query: 48_e_k27me3_131_0.465

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Matches to Query: 49_h_k36me3_12_0.534

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Matches to Query: 50_e_k9me3_10_0.467

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Summary 

Alignment 

Name BAT4_2_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.42487e-06
E-value 0.0246091
q-value 0.0492181
Overlap 5
Offset -2
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]

Matches to Query: 51_e_k4me3_308_0.533

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Matches to Query: 52_h_k9me3_8_0.467

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Matches to Query: 53_e_k36me3_205_0.530

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Matches to Query: 54_h_k9me3_7_0.470

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Matches to Query: 55_e_k9me3_142_0.470

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Matches to Query: 56_e_k9me3_112_0.472

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Matches to Query: 57_e_k36me3_220_0.528

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Matches to Query: 58_e_k27me3_65_0.473

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Summary 

Alignment 

Name NRSF_Q4_M01028_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.38666e-06
E-value 0.0157344
q-value 0.0314483
Overlap 9
Offset 6
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name PDR1_02_M01633_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.55641e-05
E-value 0.0454628
q-value 0.0454332
Overlap 7
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 59_e_k27ac_405_0.473

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Summary 

Alignment 

Name SOX9_MA0077.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.83297e-08
E-value 0.000199591
q-value 0.000396999
Overlap 9
Offset 0
Orientation Normal
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Summary 

Alignment 

Name SOX9_B1_M00410_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.6746e-07
E-value 0.00078125
q-value 0.000643537
Overlap 9
Offset 3
Orientation Normal
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Summary 

Alignment 

Name ROX1_MA0371.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.32288e-07
E-value 0.000970614
q-value 0.000643537
Overlap 9
Offset 2
Orientation Reverse Complement
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Summary 

Alignment 

Name D_MA00445.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.94474e-07
E-value 0.00144436
q-value 0.00071823
Overlap 9
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Sox30_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.02707e-06
E-value 0.0146841
q-value 0.00584151
Overlap 9
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name ROX1_Q6_M00728_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.61395e-06
E-value 0.0251614
q-value 0.00826726
Overlap 8
Offset -1
Orientation Reverse Complement
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Summary 

Alignment 

Name SOX4_01_M01308_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.96047e-06
E-value 0.0290945
q-value 0.00826726
Overlap 8
Offset -1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 60_e_k4me3_64_0.527

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Summary 

Alignment 

Name RDS1_MA0361.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.01294e-05
E-value 0.029588
q-value 0.0591759
Overlap 7
Offset 0
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 61_e_k4me3_309_0.526

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Matches to Query: 62_h_k4me3_11_0.475

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Summary 

Alignment 

Name SWI4_01_M01609_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.46246e-06
E-value 0.00427186
q-value 0.00854255
Overlap 7
Offset -1
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name SWI4_MA0401.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.00197e-05
E-value 0.0292676
q-value 0.0292636
Overlap 8
Offset -1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 63_h_k4me3_5_0.523

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Matches to Query: 64_e_k9me3_269_0.477

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Summary 

Alignment 

Name STUB1_11_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.09773e-06
E-value 0.00612747
q-value 0.0122549
Overlap 5
Offset 0
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 65_e_k4me3_70_0.479

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Matches to Query: 66_e_k27ac_480_0.479

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Matches to Query: 67_e_k9me3_225_0.479

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Matches to Query: 68_e_k27me3_277_0.479

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Matches to Query: 69_h_k27ac_13_0.520

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Summary 

Alignment 

Name IVD_4_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.79684e-06
E-value 0.0286166
q-value 0.0552865
Overlap 7
Offset -3
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 70_e_k9me3_95_0.481

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Matches to Query: 71_e_k27ac_467_0.482

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Matches to Query: 72_e_k9me3_26_0.482

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Matches to Query: 73_e_k4me3_274_0.516

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Matches to Query: 74_e_k27me3_309_0.485

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Matches to Query: 75_e_k27ac_154_0.515

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Matches to Query: 76_e_k27ac_470_0.514

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Matches to Query: 77_e_k9me3_84_0.487

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Matches to Query: 78_e_k4me1_503_0.508

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Matches to Query: 79_h_k9me3_4_0.493

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Matches to Query: 80_e_k4me1_254_0.507

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TOMTOM version
4.8.1 (Release date: Tue Feb 7 14:03:40 EST 2012)
Reference
Shobhit Gupta, JA Stamatoyannopolous, Timothy Bailey and William Stafford Noble, "Quantifying similarity between motifs", Genome Biology, 8(2):R24, 2007.
Command line summary

Background letter frequencies (from first motif database):
A: 0.295   C: 0.205   G: 0.205   T: 0.295

Result calculation took 203.159 seconds
show model parameters...

Explanation of TOMTOM Results

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The TOMTOM results consist of

Inputs

The important inputs to TOMTOM.

Query Motifs

The query motifs section lists the motifs that were searched for in the target databases as well as links to matches found.

Name
The motif name.
Alt. Name
The alternative motif name. This column may be hidden if no query motifs have an alternate name.
Website
A link to a website which has more information on the motif. This column may be hidden if no query motifs have website information.
Preview
The motif preview. On supporting browsers this will display as a motif logo, otherwise the consensus sequence will be displayed.
Matches
The number of significant matches.
List
Links to the first 20 matches
Target Databases

The target motifs section lists details on the motif databases that were specifed to search.

Database
The database name.
Number of Motifs
The number of motifs read from the motif database minus the number that had to be discarded due to conflicting ids.
Motifs Matched
The number of motifs that had a match with at least one of the query motifs.

Matches

The matches section list the group of motifs that match each query motif. For each query-target match the following information is given:

Summary Table

The summary gives the important statistics about the motif match.

Name
The name of the matched motif.
Alt. Name
The alternative name of the matched motif.
p-value
The probability that the match occurred by random chance according to the null model.
E-value
The expected number of false positives in the matches up to this point.
q-value
The minimum False Discovery Rate required to include the match.
Overlap
The number of letters that overlaped in the optimal alignment.
Offset
The offset of the query motif to the matched motif in the optimal alignment.
Orientation
The orientation of the matched motif that gave the optimal alignment. A value of "normal" means that the matched motif is as it appears in the database otherwise the matched motif has been reverse complemented.
Alignment

The image shows the alignment of the two motifs. The matched motif is shown on the top and the query motif is shown on the bottom.

Create custom LOGO

By clicking the link "Create custom LOGO ↧" a form to make custom logos will be displayed. The download button can then be clicked to generate a motif matching the selected specifications.

Image Type
Two image formats, png and eps, are avaliable. The pixel based portable network graphic (png) format is commonly used on the Internet and the Encapsulated PostScript (eps) format is more suitable for publications that might require scaling.
Error bars
Toggle error bars indicating the confidence of a motif based on the number of sites used in its creation.
SSC
Toggle adding pseudocounts for Small Sample Correction.
Flip
Toggle a full reverse complement of the alignment.
Width
Specify the width of the generated motif.
Height
Specify the height of the generated motif.